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RDKit Add Conformers

RDKit Nodes for Knime version 3.4.0.v201807311105 by NIBR

Creates a new table with multiple conformers per input molecule. Each conformer is a copy of the molecule with different coordinates assigned. Each conformer row is mapped back to the input table molecule with an identifier - usually the row id - taken from an input table column.


Input - RDKit Mol column
The input column with RDKit Molecules.
Input - Reference column (e.g. an ID)
The input column with reference data to be assigned to conformer rows.
Conformer Calculation - Number of conformers
Number of conformers to be generated.
Conformer Calculation - Maximum number of tries to generate conformers
Maximum number of tries that the RDKit will use to generate conformers.
Conformer Calculation - Random seed
A random seed to initialize random number generator.
Conformer Calculation - RMS threshold for keeping a conformer
The RMS threshold for keeping a conformer.
Output - Column name for molecules with conformers
The output column with the generated conformers.
Output - Column name for copied reference data
The output column with reference data taken from the input table.
Advanced - Use random coordinates as a starting point instead of distance geometry
Setting this flag will use random coordinates as a starting point instead of distance geometry.
Advanced - Multiplier for the size of the box for random coordinates
Specifies a multiplier for the size of the box for random coordinates.
Advanced - Perform a cleanup using UFF (Universal force field) after calculation
Set this flag to perform cleanup with UFF after the conformer's calculation. Just clear this flag to output unprocessed conformers in case you want to perform other processing on them before cleaning them up with a force field.

Input Ports

Input table with RDKit Molecules

Output Ports

Table with calculated conformers

Best Friends (Incoming)

Best Friends (Outgoing)


Update Site

To use this node in KNIME, install RDKit Nodes for Knime from the following update site:

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